// CyTargetLinker,
// a Cytoscape plugin to extend biological networks with regulatory interaction
//
// Copyright 2011-2013 Department of Bioinformatics - BiGCaT, Maastricht University
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//       http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package cytargetlinker;

import java.io.File;

import javax.swing.JMenu;

import cytargetlinker.actions.HelpAction;
import cytargetlinker.actions.LoadInteractionsAction;
import cytoscape.Cytoscape;
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.view.CyMenus;
import cytoscape.view.CytoscapeDesktop;

/**
 * Implementation of the Cytoscape Plugin class
 * for the CyTargetLinkerPlugin
 */
public class CyTargetLinkerPlugin extends CytoscapePlugin {

	private File networkDirectory;
	
	/**
	 * creates a submenu CyTargetLinker plugin in the
	 * plugin menu of Cytoscape
	 */
	public CyTargetLinkerPlugin() {
		CytoscapeDesktop desktop = Cytoscape.getDesktop();
		CyMenus menu = desktop.getCyMenus();
		JMenu pluginMenu = menu.getOperationsMenu();
		JMenu ctlMenu = new JMenu("CyTargetLinker plugin");
		ctlMenu.add(new LoadInteractionsAction(this));
		ctlMenu.add(new HelpAction());
		pluginMenu.add(ctlMenu);
	}

	public File getNetworkDirectory() {
		return networkDirectory;
	}

	public void setNetworkDirectory(File networkDirectory) {
		this.networkDirectory = networkDirectory;
	}
}